二、Detect-seq技术原理 利用了CBE过程中会产生中间产物脱氧尿嘧啶(dU)这一特点,研究人员开发了名为Detect-seq的CBE体外脱靶检测技术。该技术首先需要提取碱基编辑后的细胞的基因组DNA,然后将CBE产生的dU进行生物素(biotin)标记,用于富集目的片段;同时在dU位点的下游,将正常胞嘧啶C替换为5-醛基胞嘧啶(d5fC),随后d...
通过Detect-seq检测发现,除RNF2位点外,其它靶向位点均可以产生几十至数百个Cas9依赖型的脱靶位点(图2)。 图2 在三种不同sgRNA样品中鉴定到的Cas依赖型的脱靶位点,其中蓝色圆圈代表脱靶位点(off-targets),红色方块代表靶向位点(on-target)EMX1n=48,VEGFA_site_2 n=511,HEK293_site_4 n=245 发现了两种新型脱...
Detect-seq (dU-detection enabled by C-to-T transition during sequencing) enables off-target evaluation of programmable cytosine base editors. DNA is chemically labeled, and the editing intermediate dU is enriched for sequencing by biotin pull-down....
Cytosine base editors (CBEs) have the potential to correct human pathogenic point mutations. However, their genome-wide specificity remains poorly understood. Here we report Detect-seq for the evaluation of CBE specificity. It enables sensitive detection of CBE-induced off-target sites at the genome...
推奨:ほとんどの場合、このパラメーターにはデフォルト値を 使用する必要があります。seqdetectをオフにするのは、これ以外のチューニングで重大な照会パフォーマンス上の問題が解決できなかった場合だけにしてください。
但是,在运行时,检测到顺序检测预取的工作表现不够好时,预取类型可能从顺序检测预取切换至提前读预取。 如果此参数设为 No,那么系统会在查询执行期间对带有 INDEXDATA 选项的 INSPECT 命令、RUNSTATS 命令和所有索引扫描禁用顺序检测预取和提前读预取。但是,对于针对索引的带有 CLEANUP 选项的 REORG 命令,将 seqdetect ...
SeqX: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures. BMC Bioinformatics, 6.Biro, J. C. and Fordos, G. (2005). Seqx: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures. Bmc ...
Array comparative genomic hybridization (aCGH) is commonly used for CNV detection, but the microarray platform has a number of inherent limitations./p pResults/p pHere, we describe a method to detect copy number variation using shotgun sequencing, CNV-seq. The method is based on a robust ...
GUIDE-seq labeled and enriched double-strand breaks (DSBs) in the genome of living cells using exogenous double-stranded oligodeoxynucleotides (dsODNs) mediated by an end-joining process5. However, the high molarity of exogenous dsODNs limited its application to detect off-targets for in vivo ...
(2014), “Using RNA-seq Data to Detect Differentially Expressed Genes,” in Statistical Analysis of Next Generation Sequencing Data Springer, pp. 25–49.Lorenz, D. J., Gill, R. S., Mitra, R., and Datta, S. (2014), "Using RNA-seq Data to Detect Differentially Expressed Genes," in ...